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Mohammad T, Zolotovskaia MA, Suntsova MV, Buzdin AA. Cancer fusion transcripts with human non-coding RNAs. Front Oncol 2024; 14:1415801. [PMID: 38919532 PMCID: PMC11196610 DOI: 10.3389/fonc.2024.1415801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer chimeric, or fusion, transcripts are thought to most frequently appear due to chromosomal aberrations that combine moieties of unrelated normal genes. When being expressed, this results in chimeric RNAs having upstream and downstream parts relatively to the breakpoint position for the 5'- and 3'-fusion components, respectively. As many other types of cancer mutations, fusion genes can be of either driver or passenger type. The driver fusions may have pivotal roles in malignisation by regulating survival, growth, and proliferation of tumor cells, whereas the passenger fusions most likely have no specific function in cancer. The majority of research on fusion gene formation events is concentrated on identifying fusion proteins through chimeric transcripts. However, contemporary studies evidence that fusion events involving non-coding RNA (ncRNA) genes may also have strong oncogenic potential. In this review we highlight most frequent classes of ncRNAs fusions and summarize current understanding of their functional roles. In many cases, cancer ncRNA fusion can result in altered concentration of the non-coding RNA itself, or it can promote protein expression from the protein-coding fusion moiety. Differential splicing, in turn, can enrich the repertoire of cancer chimeric transcripts, e.g. as observed for the fusions of circular RNAs and long non-coding RNAs. These and other ncRNA fusions are being increasingly recognized as cancer biomarkers and even potential therapeutic targets. Finally, we discuss the use of ncRNA fusion genes in the context of cancer detection and therapy.
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Affiliation(s)
- Tharaa Mohammad
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Anton A. Buzdin
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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2
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Panicker S, Chengizkhan G, Gor R, Ramachandran I, Ramalingam S. Exploring the Relationship between Fusion Genes and MicroRNAs in Cancer. Cells 2023; 12:2467. [PMID: 37887311 PMCID: PMC10605240 DOI: 10.3390/cells12202467] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Fusion genes are key cancer driver genes that can be used as potential drug targets in precision therapies, and they can also serve as accurate diagnostic and prognostic biomarkers. The fusion genes can cause microRNA (miRNA/miR) aberrations in many types of cancer. Nevertheless, whether fusion genes incite miRNA aberrations as one of their many critical oncogenic functionalities for driving carcinogenesis needs further investigation. Recent discoveries of miRNA genes that are present within the regions of genomic rearrangements that initiate fusion gene-based intronic miRNA dysregulation have brought the fusion genes into the limelight and revealed their unexplored potential in the field of cancer biology. Fusion gene-based 'promoter-switch' event aberrantly activate the miRNA-related upstream regulatory signals, while fusion-based coding region alterations disrupt the original miRNA coding loci. Fusion genes can potentially regulate the miRNA aberrations regardless of the protein-coding capability of the resultant fusion transcript. Studies on out-of-frame fusion and nonrecurrent fusion genes that cause miRNA dysregulation have attracted the attention of researchers on fusion genes from an oncological perspective and therefore could have potential implications in cancer therapies. This review will provide insights into the role of fusion genes and miRNAs, and their possible interrelationships in cancer.
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Affiliation(s)
- Saurav Panicker
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, India; (S.P.); (R.G.)
| | - Gautham Chengizkhan
- Department of Endocrinology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai 600113, Tamil Nadu, India;
| | - Ravi Gor
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, India; (S.P.); (R.G.)
| | - Ilangovan Ramachandran
- Department of Endocrinology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai 600113, Tamil Nadu, India;
| | - Satish Ramalingam
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu 603203, Tamil Nadu, India; (S.P.); (R.G.)
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3
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MicroRNAs and the Diagnosis of Childhood Acute Lymphoblastic Leukemia: Systematic Review, Meta-Analysis and Re-Analysis with Novel Small RNA-Seq Tools. Cancers (Basel) 2022; 14:cancers14163976. [PMID: 36010971 PMCID: PMC9406077 DOI: 10.3390/cancers14163976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary MicroRNAs (miRNAs) have been under the spotlight for the last three decades. These non-coding RNAs seem to be dynamic regulators of mRNA stability and translation, in addition to interfering with transcription. Circulating miRNAs play a critical role in cell-to-cell interplay; therefore, they can serve as disease biomarkers. Meta-analysis of published data revealed that the CC genotype of rs4938723 in pri-miR-34b/c and the TT genotype of rs543412 in miR-100 confer protection against acute lymphoblastic leukemia (ALL) in children. Reanalysis of small RNA-seq data with novel tools identified significantly overexpressed members of the miR-128, miR-181, miR-130 and miR-17 families and significantly lower expression of miR-30, miR-24-2 and miR143~145 clusters, miR-574 and miR-618 in pediatric T-ALL cases compared with controls. Inconsistencies in methodology and study designs in most published material preclude reproducibility, and further cohort studies need to be conducted in order to empower novel tools, such as ALLSorts and RNAseqCNV. Abstract MicroRNAs (miRNAs) have been implicated in childhood acute lymphoblastic leukemia (ALL) pathogenesis. We performed a systematic review and meta-analysis of miRNA single-nucleotide polymorphisms (SNPs) in childhood ALL compared with healthy children, which revealed (i) that the CC genotype of rs4938723 in pri-miR-34b/c and the TT genotype of rs543412 in miR-100 confer protection against ALL occurrence in children; (ii) no significant association between rs2910164 genotypes in miR-146a and childhood ALL; and (iii) SNPs in DROSHA, miR-449b, miR-938, miR-3117 and miR-3689d-2 genes seem to be associated with susceptibility to B-ALL in childhood. A review of published literature on differential expression of miRNAs in children with ALL compared with controls revealed a significant upregulation of the miR-128 family, miR-130b, miR-155, miR-181 family, miR-210, miR-222, miR-363 and miR-708, along with significant downregulation of miR-143 and miR-148a, seem to have a definite role in childhood ALL development. MicroRNA signatures among childhood ALL subtypes, along with differential miRNA expression patterns between B-ALL and T-ALL cases, were scrutinized. With respect to T-ALL pediatric cases, we reanalyzed RNA-seq datasets with a robust and sensitive pipeline and confirmed the significant differential expression of hsa-miR-16-5p, hsa-miR-19b-3p, hsa-miR-92a-2-5p, hsa-miR-128-3p (ranked first), hsa-miR-130b-3p and -5p, hsa-miR-181a-5p, -2-3p and -3p, hsa-miR-181b-5p and -3p, hsa-miR-145-5p and hsa-miR-574-3p, as described in the literature, along with novel identified miRNAs.
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4
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Sbirkov Y, Vergov B, Mehterov N, Sarafian V. miRNAs in Lymphocytic Leukaemias-The miRror of Drug Resistance. Int J Mol Sci 2022; 23:ijms23094657. [PMID: 35563051 PMCID: PMC9103677 DOI: 10.3390/ijms23094657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 02/04/2023] Open
Abstract
Refractory disease and relapse remain the main causes of cancer therapy failure. Refined risk stratification, treatment regimens and improved early diagnosis and detection of minimal residual disease have increased cure rates in malignancies like childhood acute lymphoblastic leukaemia (ALL) to 90%. Nevertheless, overall survival in the context of drug resistance remains poor. The regulatory role of micro RNAs (miRNAs) in cell differentiation, homeostasis and tumorigenesis has been under extensive investigation in different cancers. There is accumulating data demonstrating the significance of miRNAs for therapy outcomes in lymphoid malignancies and some direct demonstrations of the interplay between these small molecules and drug response. Here, we summarise miRNAs' impact on chemotherapy resistance in adult and paediatric ALL and chronic lymphocytic leukaemia (CLL). The main focus of this review is on the modulation of particular signaling pathways like PI3K-AKT, transcription factors such as NF-κB, and apoptotic mediators, all of which are bona fide and pivotal elements orchestrating the survival of malignant lymphocytic cells. Finally, we discuss the attractive strategy of using mimics, antimiRs and other molecular approaches pointing at miRNAs as promising therapeutic targets. Such novel strategies to circumvent ALL and CLL resistance networks may potentially improve patients' responses and survival rates.
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Affiliation(s)
- Yordan Sbirkov
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
- Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
- Correspondence: (Y.S.); (V.S.)
| | - Bozhidar Vergov
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
- Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
- Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
- Correspondence: (Y.S.); (V.S.)
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5
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Peng B, Theng PY, Le MTN. Essential functions of miR-125b in cancer. Cell Prolif 2020; 54:e12913. [PMID: 33332677 PMCID: PMC7848968 DOI: 10.1111/cpr.12913] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/20/2020] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are small and highly conserved non-coding RNAs that silence target mRNAs, and compelling evidence suggests that they play an essential role in the pathogenesis of human diseases, especially cancer. miR-125b, which is the mammalian orthologue of the first discovered miRNA lin-4 in Caenorhabditis elegans, is one of the most important miRNAs that regulate various physiological and pathological processes. The role of miR-125b in many types of cancer has been well established, and so here we review the current knowledge of how miR-125b is deregulated in different types of cancer; its oncogenic and/or tumour-suppressive roles in tumourigenesis and cancer progression; and its regulation with regard to treatment response, all of which are underlined in multiple studies. The emerging information that elucidates the essential functions of miR-125b might help support its potentiality as a diagnostic and prognostic biomarker as well as an effective therapeutic tool against cancer.
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Affiliation(s)
- Boya Peng
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biomedical Sciences, School of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong.,N.1 Institute for Health, National University of Singapore, Singapore, Singapore
| | - Poh Ying Theng
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Minh T N Le
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biomedical Sciences, School of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong.,N.1 Institute for Health, National University of Singapore, Singapore, Singapore.,City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
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6
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Han C, Sun LY, Wang WT, Sun YM, Chen YQ. Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications. J Mol Cell Biol 2020; 11:886-898. [PMID: 31361891 PMCID: PMC6884712 DOI: 10.1093/jmcb/mjz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 12/25/2022] Open
Abstract
Chromosomal translocation leads to the juxtaposition of two otherwise separate DNA loci, which could result in gene fusion. These rearrangements at the DNA level are catastrophic events and often have causal roles in tumorigenesis. The oncogenic DNA messages are transferred to RNA molecules, which are in most cases translated into cancerous fusion proteins. Gene expression programs and signaling pathways are altered in these cytogenetically abnormal contexts. Notably, non-coding RNAs have attracted increasing attention and are believed to be tightly associated with chromosome-rearranged cancers. These RNAs not only function as modulators in downstream pathways but also directly affect chromosomal translocation or the associated products. This review summarizes recent research advances on the relationship between non-coding RNAs and chromosomal translocations and on diverse functions of non-coding RNAs in cancers with chromosomal rearrangements.
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Affiliation(s)
- Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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7
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Gutierrez-Camino A, Garcia-Obregon S, Lopez-Lopez E, Astigarraga I, Garcia-Orad A. miRNA deregulation in childhood acute lymphoblastic leukemia: a systematic review. Epigenomics 2019; 12:69-80. [PMID: 31833405 DOI: 10.2217/epi-2019-0154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Despite remarkable improvements in survival of childhood acute lymphoblastic leukemia (ALL), nonresponding or relapsing patients still represent one of the most frequent causes of death by disease in children. Accurate patient risk stratification based on genetic markers could increases survival rates. miRNAs can represent novel candidates with diagnostic, predictive and prognostic potential; however, many groups investigated their involvement with contradictory results. Aim: To clarify the role of miRNAs as biomarkers through a systematic review. Results: From a revision of 45 manuscripts, we found that miR-128 and miR-181 overexpression could represent markers for ALL diagnosis and underexpression of miR-708 and miR-99a could be markers for bad prognosis. Conclusion: These signatures could refine classification and risk stratification of patients and improve ALL outcome.
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Affiliation(s)
- Angela Gutierrez-Camino
- Department of Genetics, Physical Anthropology & Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain.,BioCruces Bizkaia Health Research Institute, Pediatric Oncology Group, Barakaldo, 48903, Spain.,Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, Montreal, QC H3T 1C5, Canada
| | - Susana Garcia-Obregon
- BioCruces Bizkaia Health Research Institute, Pediatric Oncology Group, Barakaldo, 48903, Spain
| | - Elixabet Lopez-Lopez
- Department of Genetics, Physical Anthropology & Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain.,BioCruces Bizkaia Health Research Institute, Pediatric Oncology Group, Barakaldo, 48903, Spain
| | - Itziar Astigarraga
- BioCruces Bizkaia Health Research Institute, Pediatric Oncology Group, Barakaldo, 48903, Spain.,Department of Pediatrics, University Hospital Cruces, Barakaldo, 48903, Spain.,Department of Pediatrics, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - Africa Garcia-Orad
- Department of Genetics, Physical Anthropology & Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain.,BioCruces Bizkaia Health Research Institute, Pediatric Oncology Group, Barakaldo, 48903, Spain
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8
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Adhikary J, Chakraborty S, Dalal S, Basu S, Dey A, Ghosh A. Circular PVT1: an oncogenic non-coding RNA with emerging clinical importance. J Clin Pathol 2019; 72:513-519. [PMID: 31154423 DOI: 10.1136/jclinpath-2019-205891] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022]
Abstract
The importance of circular RNAs (circRNAs) in pathological processes like cancer is evident. Among the circRNAs, recent studies have brought circPVT1 under focus as the most potent oncogenic non-coding RNA. Recent studies on various aspects of circPVT1, including its biogenesis, molecular alteration and its probable role in oncogenesis, have been conducted for research and clinical interest. In this review, a first attempt has been made to summarise the available data on circPVT1 from PubMed and other relevant databases with special emphasis on its role in development, progression and prognosis of various malignant conditions. CircPVT1 is derived from the same genetic locus encoding for long non-coding RNA lncPVT1; however, existing literature suggested circPVT1 and lncPVT1 are transcripted independently by different promoters. The interaction between circRNA and microRNA has been highlighted in majority of the few malignancies in which circPVT1 was studied. Besides its importance in diagnostic and prognostic procedures, circPVT1 seemed to have huge therapeutic potential as evident from differential drug response of cancer cell line as well as primary tumors depending on expression level of the candidate. circPVT1 in cancer therapeutics might be promising as a biomarker to make the existing treatment protocol more effective and also as potential target for designing novel therapeutic intervention.
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Affiliation(s)
- Jayashree Adhikary
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
| | | | - Subhamita Dalal
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
| | | | - Abhijit Dey
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
| | - Amlan Ghosh
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
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9
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El-Khazragy N, Elshimy AA, Hassan SS, Matbouly S, Safwat G, Zannoun M, Riad RA. Dysregulation of miR-125b predicts poor response to therapy in pediatric acute lymphoblastic leukemia. J Cell Biochem 2019; 120:7428-7438. [PMID: 30390332 DOI: 10.1002/jcb.28017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/15/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is the most well-known sort of leukemia in children. In spite of favorable survival rates, some patients relapse and achieve a poor outcome. METHODS We analyzed miR-125b and Bcl-2 expressions in pediatric patients with ALL and evaluated their clinical utility as molecular markers for the prediction of disease outcomes. RESULTS Downregulation of miR-125b and increased Bcl-2 expression levels in pediatric patients with ALL were associated with poor prognosis at diagnosis. At day 28 of induction, miR-125b was significantly increased, whereas Bcl-2 was downregulated. Loss of miR-125b during diagnosis and its elevation after therapy are strongly correlated with short leukemia-free survival and worse survival. Moreover, the combination of miR-125b with Bcl-2 markers can clearly enhance the prediction of the disease outcome. Finally, a univariate analysis highlighted the independent prognostic value of miR-125 in a pediatric patient with ALL. CONCLUSIONS miR-125b and Bcl-2 together are potent predictors for the prognosis and, therefore, can be used as therapeutic targets in childhood ALL.
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Affiliation(s)
- Nashwa El-Khazragy
- Department of Clinical Pathology and Hematology, Faculty of Medicine, Ain Shams Medical Research Institute (MASRI), Ain Shams University, Cairo, Egypt.,Former Department of Biomedical Research, Armed Forces College of Medicine (AFCM), Cairo, Egypt
| | - Amal Ali Elshimy
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, New Giza University, Cairo, Egypt
| | - Safaa Shawky Hassan
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Safa Matbouly
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Gehan Safwat
- Department of Cancer Biology, Faculty of Biotechnology, October University for Modern Sciences and Art (MSA) University, Cairo, Egypt
| | - Mohamed Zannoun
- Department of Pediatrics, Faculty of Medicine, Al Azhar University, Cairo, Egypt
| | - Ramez A Riad
- Department of Biotechnology and Molecular Biology, Global Research Lab, Cairo, Egypt
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10
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Rovira C. miRNA-convergent gene fusions. Mol Cell Oncol 2018; 5:e1406433. [PMID: 29404401 DOI: 10.1080/23723556.2017.1406433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 11/13/2017] [Accepted: 11/13/2017] [Indexed: 02/05/2023]
Abstract
In a recent study published in Nature Communications, we showed that intron-encoded microRNA genes (miRNA) are frequent partners of fusion genes in the cancer genome. Analyzed from a functional rather than structural perspective, these rearrangements represent a new class of fusions we called "miRNA-convergent fusions".
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Affiliation(s)
- Carlos Rovira
- Department of Clinical Sciences Lund, Division of Oncology and Pathology and BioCARE, Strategic Cancer Research Program, Lund University, Lund, Sweden
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11
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Frequent miRNA-convergent fusion gene events in breast cancer. Nat Commun 2017; 8:788. [PMID: 28983113 PMCID: PMC5629207 DOI: 10.1038/s41467-017-01176-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/24/2017] [Indexed: 12/18/2022] Open
Abstract
Studies of fusion genes have mainly focused on the formation of fusions that result in the production of hybrid proteins or, alternatively, on promoter-switching events that put a gene under the control of aberrant signals. However, gene fusions may also disrupt the transcriptional control of genes that are encoded in introns downstream of the breakpoint. By ignoring structural constraints of the transcribed fusions, we highlight the importance of a largely unexplored function of fusion genes. Here, we show, using breast cancer as an example, that miRNA host genes are specifically enriched in fusion genes and that many different, low-frequency, 5ʹ partners may deregulate the same miRNA irrespective of the coding potential of the fusion transcript. These results indicate that the concept of recurrence, defined by the rate of functionally important aberrations, needs to be revised to encompass convergent fusions that affect a miRNA independently of transcript structure and protein-coding potential. Fusion gene research traditionally focuses on fusions that result in hybrid proteins or promoter switching events. Here, the authors demonstrate enrichment of fusions in miRNA host genes in breast cancer, highlighting that disparate fusions could have convergent impact on miRNA.
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12
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Piatopoulou D, Avgeris M, Marmarinos A, Xagorari M, Baka M, Doganis D, Kossiva L, Scorilas A, Gourgiotis D. miR-125b predicts childhood acute lymphoblastic leukaemia poor response to BFM chemotherapy treatment. Br J Cancer 2017; 117:801-812. [PMID: 28787435 PMCID: PMC5589998 DOI: 10.1038/bjc.2017.256] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/04/2017] [Accepted: 07/10/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Despite the favourable survival rates of childhood acute lymphoblastic leukaemia (ALL), a significant number of patients present resistance to antileukaemic agents and dismal prognosis. In this study, we analysed miR-125b expression in childhood ALL and evaluated its clinical utility for patients treated with Berlin-Frankfurt-Münster (BFM) protocol. METHODS The study included 272 bone marrow specimens obtained on diagnosis and on BFM day 33 from 125 patients and 64 healthy children. Following extraction, RNA was polyadenylated and reverse transcribed. miR-125b levels were quantified by quantitative PCR. Cytogenetics, immunohistotype and MRD were analysed according to international guidelines. RESULTS Downregulated miR-125b levels were detected in childhood ALL patients and correlated with adverse prognosis. Following BFM induction, miR-125b levels were significantly increased, however, elevated day 33/diagnosis miR-125b ratio was associated with unfavourable disease features. Loss of miR-125b during diagnosis and higher day 33/diagnosis ratio were correlated with stronger risk for disease short-term relapse and patients' worse survival. Moreover, multivariate regression models highlighted the independent prognostic value of miR-125b for childhood ALL. Finally, the combination of miR-125b with clinically used disease markers clearly enhanced the prediction of patients' resistance to BFM chemotherapy. CONCLUSIONS miR-125b significantly improves the prognosis of childhood ALL patients' outcome under BFM treatment.
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Affiliation(s)
- Despina Piatopoulou
- Laboratory of Clinical Biochemistry—Molecular Diagnostics, 2nd Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, ‘P & A Kyriakou’ Children’s Hospital, Levadias 13 Street, Athens 11527, Greece
| | - Margaritis Avgeris
- Faculty of Biology, Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Antonios Marmarinos
- Laboratory of Clinical Biochemistry—Molecular Diagnostics, 2nd Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, ‘P & A Kyriakou’ Children’s Hospital, Levadias 13 Street, Athens 11527, Greece
| | - Marieta Xagorari
- Laboratory of Clinical Biochemistry—Molecular Diagnostics, 2nd Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, ‘P & A Kyriakou’ Children’s Hospital, Levadias 13 Street, Athens 11527, Greece
| | - Margarita Baka
- Department of Pediatric Oncology, ‘P & A Kyriakou’ Children’s Hospital, Thivon & Levadias Street, Athens 11527, Greece
| | - Dimitrios Doganis
- Department of Pediatric Oncology, ‘P & A Kyriakou’ Children’s Hospital, Thivon & Levadias Street, Athens 11527, Greece
| | - Lydia Kossiva
- 2nd Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, ‘P & A Kyriakou’ Children’s Hospital, Levadias 13 Street, Athens 11527, Greece
| | - Andreas Scorilas
- Faculty of Biology, Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Dimitrios Gourgiotis
- Laboratory of Clinical Biochemistry—Molecular Diagnostics, 2nd Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, ‘P & A Kyriakou’ Children’s Hospital, Levadias 13 Street, Athens 11527, Greece
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Knackmuss U, Lindner SE, Aneichyk T, Kotkamp B, Knust Z, Villunger A, Herzog S. MAP3K11 is a tumor suppressor targeted by the oncomiR miR-125b in early B cells. Cell Death Differ 2016; 23:242-52. [PMID: 26138442 PMCID: PMC4678593 DOI: 10.1038/cdd.2015.87] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 05/05/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small, non-coding RNAs that posttranscriptionally regulate gene expression and thereby control most, if not all, biological processes. Aberrant miRNA expression has been linked to a variety of human diseases including cancer, but the underlying molecular mechanism often remains unclear. Here we have screened a miRNA expression library in a growth factor-dependent mouse pre-B-cell system to identify miRNAs with oncogenic activity. We show that miR-125b is sufficient to render pre-B cells growth factor independent and demonstrate that continuous expression of miR-125b is necessary to keep these cells in a transformed state. Mechanistically, we find that the expression of miR-125b protects against apoptosis induced by growth factor withdrawal, and that it blocks the differentiation of pre-B to immature B cells. In consequence, miR-125b-transformed cells maintain expression of their pre-B-cell receptor that provides signals for continuous proliferation and survival even in the absence of growth factor. Employing microarray analysis, we identified numerous targets of miR-125b, but only reconstitution of MAP3K11, a critical regulator of mitogen- and stress-activated kinase signaling, interferes with the cellular fitness of the transformed cells. Together, this indicates that MAP3K11 might function as an important tumor suppressor neutralized by oncomiR-125b in B-cell leukemia.
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Affiliation(s)
- U Knackmuss
- Centre for Biological Signalling Studies (bioss), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - S E Lindner
- Division of Developmental Immunology, Biocenter Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - T Aneichyk
- Division of Molecular Pathophysiology, Biocenter Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - B Kotkamp
- Centre for Biological Signalling Studies (bioss), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Z Knust
- Centre for Biological Signalling Studies (bioss), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - A Villunger
- Division of Developmental Immunology, Biocenter Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - S Herzog
- Centre for Biological Signalling Studies (bioss), Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Division of Developmental Immunology, Biocenter Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
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14
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Luan C, Yang Z, Chen B. The functional role of microRNA in acute lymphoblastic leukemia: relevance for diagnosis, differential diagnosis, prognosis, and therapy. Onco Targets Ther 2015; 8:2903-14. [PMID: 26508875 PMCID: PMC4610789 DOI: 10.2147/ott.s92470] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs), a new class of noncoding RNAs, which can hybridize to target messenger RNAs and regulate their expression posttranscriptionally, express differentially in distinct stages of lymphopoiesis and influence the direction of lymphoid precursor maturation. Hence, there is aberrant expression of miRNAs involved in malignant lymphopoiesis, and these aberrations can be used as signatures of acute lymphoblastic leukemia (ALL) with different subtypes. In addition, changes in the expression of several miRNAs may have functional relevance with leukemogenesis or drug resistance. As a result, the reversal of the expression of these miRNAs may alleviate the disease to some extent and improve clinical outcomes. However, among the studies of miRNAs, there are still some problems that need to be solved to understand the function of miRNAs in ALL more thoroughly.
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Affiliation(s)
- Chengxin Luan
- Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, People's Republic of China
| | - Zixue Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Baoan Chen
- Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, People's Republic of China
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15
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Abstract
The oncomir microRNA-125b (miR-125b) is upregulated in a variety of human neoplastic blood disorders and constitutive upregulation of miR-125b in mice can promote myeloid and B-cell leukemia. We found that miR-125b promotes myeloid and B-cell neoplasm by inducing tumorigenesis in hematopoietic progenitor cells. Our study demonstrates that miR-125b induces myeloid leukemia by enhancing myeloid progenitor output from stem cells as well as inducing immortality, self-renewal, and tumorigenesis in myeloid progenitors. Through functional and genetic analyses, we demonstrated that miR-125b induces myeloid and B-cell leukemia by inhibiting interferon regulatory factor 4 (IRF4) but through distinct mechanisms; it induces myeloid leukemia through repressing IRF4 at the messenger RNA (mRNA) level without altering the genomic DNA and induces B-cell leukemia via genetic deletion of the gene encoding IRF4.
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16
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Inoue D, Kitaura J, Togami K, Nishimura K, Enomoto Y, Uchida T, Kagiyama Y, Kawabata KC, Nakahara F, Izawa K, Oki T, Maehara A, Isobe M, Tsuchiya A, Harada Y, Harada H, Ochiya T, Aburatani H, Kimura H, Thol F, Heuser M, Levine RL, Abdel-Wahab O, Kitamura T. Myelodysplastic syndromes are induced by histone methylation–altering ASXL1 mutations. J Clin Invest 2014; 123:4627-40. [PMID: 24216483 DOI: 10.1172/jci70739] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/08/2013] [Indexed: 01/10/2023] Open
Abstract
Recurrent mutations in the gene encoding additional sex combs-like 1 (ASXL1) are found in various hematologic malignancies and associated with poor prognosis. In particular, ASXL1 mutations are common in patients with hematologic malignancies associated with myelodysplasia, including myelodysplastic syndromes (MDSs), and chronic myelomonocytic leukemia. Although loss-of-function ASXL1 mutations promote myeloid transformation, a large subset of ASXL1 mutations is thought to result in stable truncation of ASXL1. Here we demonstrate that C-terminal–truncating Asxl1 mutations (ASXL1-MTs) inhibited myeloid differentiation and induced MDS-like disease in mice. ASXL1-MT mice displayed features of human-associated MDS, including multi-lineage myelodysplasia, pancytopenia, and occasional progression to overt leukemia. ASXL1-MT resulted in derepression of homeobox A9 (Hoxa9) and microRNA-125a (miR-125a) expression through inhibition of polycomb repressive complex 2–mediated (PRC2-mediated) methylation of histone H3K27. miR-125a reduced expression of C-type lectin domain family 5, member a (Clec5a), which is involved in myeloid differentiation. In addition, HOXA9 expression was high in MDS patients with ASXL1-MT, while CLEC5A expression was generally low. Thus, ASXL1-MT–induced MDS-like disease in mice is associated with derepression of Hoxa9 and miR-125a and with Clec5a dysregulation. Our data provide evidence for an axis of MDS pathogenesis that implicates both ASXL1 mutations and miR-125a as therapeutic targets in MDS.
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17
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Aberrant BLID expression is associated with breast cancer progression. Tumour Biol 2014; 35:5449-52. [PMID: 24532431 DOI: 10.1007/s13277-014-1710-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 01/29/2014] [Indexed: 12/20/2022] Open
Abstract
In our previous study, we have found that BH3-like motif containing, cell death inducer (BLID) was a tumor suppressor in breast cancer, and its downregulation was correlated with both poor disease-free and overall survival. In the present study, we aimed to explore the possible role of BLID in breast cancer progression. We found that BLID was strongly expressed in all normal breast tissues, and it became lower and wreaker gradually in the progression from normal, UDH (usual ductal hyperplasia), ADH (atypical ductal hyperplasia), and DCIS (ductal carcinoma in situ) to breast cancer. Statistical analysis demonstrated significant different BLID expressions between proliferative and cancerous breast lesions. Our data suggested that loss of BLID may contribute to the progression of intraductal proliferation lesions to breast cancer. Our finding gives a new clue that BLID might be a potential indicator for progression of breast cancer in the future.
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18
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Chapiro E, Radford-Weiss I, Cung HA, Dastugue N, Nadal N, Taviaux S, Barin C, Struski S, Talmant P, Vandenberghe P, Mozziconacci MJ, Tigaud I, Lefebvre C, Penther D, Bastard C, Lippert E, Mugneret F, Romana S, Bernard OA, Harrison CJ, Russell LJ, Nguyen-Khac F. Chromosomal translocations involving the IGH@ locus in B-cell precursor acute lymphoblastic leukemia: 29 new cases and a review of the literature. Cancer Genet 2013; 206:162-73. [DOI: 10.1016/j.cancergen.2013.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 04/23/2013] [Accepted: 04/23/2013] [Indexed: 01/07/2023]
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19
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Abstract
Yin and Yang are two complementary forces that together describe the nature of real-world elements. Yin is the dark side; Yang is the light side. We describe microRNAs having both Yin and Yang characteristics because they can contribute to normal function (Yang) but also to autoimmunity, myeloproliferation, and cancer (Yin). We have been working on a number of microRNAs that have these dual characteristics and here we focus on two, miR-125b and miR-146a. We have concentrated on these two RNAs because we have very extensive knowledge of them, much of it from our laboratory, and also because they provide a strong contrast: the effects of overexpression of miR-125b are rapid, suggesting that it acts directly, whereas the effects of miR-146a are slow to develop, suggesting that they arise from chronic alterations in cellular behavior.
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Affiliation(s)
- Alex Yick-Lun So
- Department of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Jimmy Zhao
- Department of Biology, California Institute of Technology, Pasadena, CA, USA
| | - David Baltimore
- Department of Biology, California Institute of Technology, Pasadena, CA, USA
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20
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Chung SS, Hu W, Park CY. The Role of MicroRNAs in Hematopoietic Stem Cell and Leukemic Stem Cell Function. Ther Adv Hematol 2013; 2:317-34. [PMID: 23556099 DOI: 10.1177/2040620711410772] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are defined by their ability to self-renew and reconstitute all elements of the hematopoietic system. Acute myeloid leukemia (AML) is thought to arise from, and be maintained by, leukemic stem cells (LSCs), which exhibit similar features to HSCs, including the abilities to self-renew and differentiate into non-self-renewing cells. Acquisition of stem-cell-like characteristics by the LSCs is likely mediated in part by molecular mechanisms that normally regulate HSC function. Thus, understanding the shared and unique aspects of the molecular regulation of these cell populations will be important to understanding the relationship between normal hematopoiesis and leukemogenesis. MicroRNAs (miRNAs) are small noncoding RNAs that act at the posttranscriptional level to regulate protein expression. Unfortunately, most investigations of the role of miRNAs in normal hematopoiesis have been restricted to studies of their effects on lineage commitment in progenitors and mature effector cell function, but not on HSCs. Recent studies have identified miRNAs that enhance HSC function, and an abundance of profiling studies using primary AML samples have identified dysregulated miRNAs that may target genes implicated in self-renewal (HOX genes, P53, and PTEN), thus providing a potential link between normal and malignant stem cells. While these studies as well as recent in vivo models of miRNA-induced leukemogenesis (e.g. miR-29a, miR-125b) suggest a role for miRNAs in the development of AML, future studies using serial transplantation of primary AML blasts, from both mouse models and primary human AML specimens, will be necessary to assess the roles of miRNAs in LSC biology.
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Affiliation(s)
- Stephen S Chung
- Human Oncology and Pathogenesis Program and Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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21
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Sun YM, Lin KY, Chen YQ. Diverse functions of miR-125 family in different cell contexts. J Hematol Oncol 2013; 6:6. [PMID: 23321005 PMCID: PMC3566921 DOI: 10.1186/1756-8722-6-6] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/10/2013] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are emerging as a novel class of non-coding RNA molecules that regulate gene expression at a post-transcriptional level. More than 1000 miRNAs have been identified in human cells to date, and they are reported to play important roles in normal cell homeostasis, cell metastasis and disease pathogensis and progression. MiR-125, which is a highly conserved miRNA throughout diverse species from nematode to humans, consists of three homologs hsa-miR-125a, hsa-miR-125b-1 and hsa-miR-125-2. Members of this family have been validated to be down-regulated, exhibiting its disease-suppressing properties in many different types of diseases, while they also have disease-promoting functions in certain contexts. MiR-125 targets a number of genes such as transcription factors, matrix-metalloprotease, members of Bcl-2 family and others, aberrance of which may lead to abnormal proliferation, metastasis and invasion of cells, even carcinomas. Furthermore, miR-125 plays a crucial role in immunological host defense, especially in response to bacterial or viral infections. In this review, we summarize the implication of miR-125 family in disease suppression and promotion, focusing on carcinoma and host immune responses. We also discussed the potential of this miRNA family as promising biomarkers and therapeutic targets for different diseases in future.
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Affiliation(s)
- Yu-Meng Sun
- Key Laboratory of Gene Engineering of Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Biotechnology Research Center, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
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22
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Enomoto Y, Kitaura J, Shimanuki M, Kato N, Nishimura K, Takahashi M, Nakakuma H, Kitamura T, Sonoki T. MicroRNA-125b-1 accelerates a C-terminal mutant of C/EBPα (C/EBPα-C(m))-induced myeloid leukemia. Int J Hematol 2012; 96:334-41. [PMID: 22843432 DOI: 10.1007/s12185-012-1143-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Revised: 07/02/2012] [Accepted: 07/02/2012] [Indexed: 01/15/2023]
Abstract
MicroRNA-125b-1 (miR-125b-1) is a target of the chromosomal translocations t(11;14)(q24;q32) and t(2;11)(p21;q23), which are found in human B-lymphoid and myeloid malignancies, respectively. These translocations result in overexpression of mature miR-125b, consisting of 22 nucleotides. To analyze the role of miR-125b-1 in leukemogenesis, we created a bone marrow transplantation model using a retrovirus vector containing GFP expression elements. Sole transduction of miR-125b-1 into bone marrow cells resulted in expansion of hematopoietic cells expressing GFP. Compared with cells lacking GFP expression, we observed that GFP(+)/CD11b(+) or GFP(+)/Gr(-)1(+) cells were increased in the bone marrow and spleen. Although previous studies reported sole induction of miR-125b-induced leukemia, we did not find leukemic transformation in our model. Transduction of miR-125b-1 did accelerate myeloid tumors induced by a C-terminal mutant of CAAT-enhancer binding protein (C/EBPα-C(m)), a class II-like mutation. As miR-125b has been shown to hasten the development of leukemia in a BCR/ABL-transduced animal model, our present results support the conclusion that overexpression of miR-125b cooperates with other genetic alterations in the pathogenesis of myeloid malignancies.
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Affiliation(s)
- Yutaka Enomoto
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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23
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Florean C, Schnekenburger M, Grandjenette C, Dicato M, Diederich M. Epigenomics of leukemia: from mechanisms to therapeutic applications. Epigenomics 2012; 3:581-609. [PMID: 22126248 DOI: 10.2217/epi.11.73] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Leukemogenesis is a multistep process in which successive transformational events enhance the ability of a clonal population arising from hematopoietic progenitor cells to proliferate, differentiate and survive. Clinically and pathologically, leukemia is subdivided into four main categories: chronic lymphocytic leukemia, chronic myeloid leukemia, acute lymphocytic leukemia and acute myeloid leukemia. Leukemia has been previously considered only as a genetic disease. However, in recent years, significant advances have been made in the elucidation of the leukemogenesis-associated processes. Thus, we have come to understand that epigenetic alterations including DNA methylation, histone modifications and miRNA are involved in the permanent changes of gene expression controlling the leukemia phenotype. In this article, we will focus on the epigenetic defects associated with leukemia and their implications as biomarkers for diagnostic, prognostic and therapeutic applications.
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Affiliation(s)
- Cristina Florean
- Laboratoire de Biologie Moléculaire et Cellulaire de Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg
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24
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B-cell regulator of immunoglobulin heavy-chain transcription (Bright)/ARID3a is a direct target of the oncomir microRNA-125b in progenitor B-cells. Leukemia 2012; 26:2224-32. [PMID: 22469780 DOI: 10.1038/leu.2012.95] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
B-cell acute lymphoblastic leukemia (B-ALL) is often associated with chromosomal translocations leading to the deregulation of proto-oncogenes. MicroRNAs can also be affected by chromosomal alterations and thus contribute to carcinogenesis. The microRNA, miR-125b-1, is overexpressed in B-ALL cases with the t(11;14)(q24;q32) translocation; therefore, we sought to determine the role of this microRNA in B-cell fate. We used murine pre-BI cells alongside murine and human leukemic B-cell lines to show that miR-125b expression enhances proliferation by targeting B-cell regulator of immunoglobulin heavy-chain transcription (Bright)/ARID3a, an activator of immunoglobulin heavy-chain transcription. Accordingly, this target gene was downregulated in B-ALL patients with the t(11;14)(q24;q32) translocation. Repression of Bright/ARID3a blocked differentiation and conferred a survival advantage to Ba/F3 cells under interleukin-3 starvation. In addition, overexpression of miR-125b protected pre-BI and leukemic B-cell lines from apoptosis by blockade of caspase activation by a mechanism that was independent of p53 and BAK1. In summary, miR-125b can act as an oncogene in B-ALL by targeting ARID3a and mediating its repression, thus leading to a blockage in differentiation, increased proliferation and inhibition of apoptosis.
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25
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Abstract
MiR-125 is a highly conserved microRNA throughout many different species from nematode to humans. In humans, there are three homologs (hsa-miR-125b-1, hsa-miR-125b-2 and hsa-miR-125a). Here we review a recent research on the role of miR-125 in normal and malignant hematopoietic cells. Its high expression in hematopoietic stem cells (HSCs) enhances self-renewal and survival. Its expression in specific subtypes of myeloid and lymphoid leukemias provides resistance to apoptosis and blocks further differentiation. A direct oncogenic role in the hematopoietic system has recently been demonstrated by several mouse models. Targets of miR-125b include key proteins regulating apoptosis, innate immunity, inflammation and hematopoietic differentiation.
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26
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de Oliveira JC, Scrideli CA, Brassesco MS, Morales AG, Pezuk JA, Queiroz RDP, Yunes JA, Brandalise SR, Tone LG. Differential miRNA expression in childhood acute lymphoblastic leukemia and association with clinical and biological features. Leuk Res 2011; 36:293-8. [PMID: 22099053 DOI: 10.1016/j.leukres.2011.10.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/27/2011] [Accepted: 10/07/2011] [Indexed: 01/02/2023]
Abstract
The present study aimed to analyze the expression profile of the microRNAs previously described as associated with childhood ALL, miR-92a, miR-100, miR-125a-5p, miR-128a, miR-181b, miR-196b and let-7e, and their association with biological/prognostic features in 128 consecutive samples of childhood acute lymphoblastic leukemia (ALL) by quantitative real-time PCR. A significant association was observed between higher expression levels of miR-196b and T-ALL, miR-100 and patients with low white blood cell count at diagnosis and t(12;21) positive ALL. These findings suggest a potential activity of these microRNAs in pediatric ALL biology.
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27
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Enomoto Y, Kitaura J, Hatakeyama K, Watanuki J, Akasaka T, Kato N, Shimanuki M, Nishimura K, Takahashi M, Taniwaki M, Haferlach C, Siebert R, Dyer MJS, Asou N, Aburatani H, Nakakuma H, Kitamura T, Sonoki T. Eμ/miR-125b transgenic mice develop lethal B-cell malignancies. Leukemia 2011; 25:1849-56. [DOI: 10.1038/leu.2011.166] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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28
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MicroRNA-125b expands hematopoietic stem cells and enriches for the lymphoid-balanced and lymphoid-biased subsets. Proc Natl Acad Sci U S A 2010; 107:21505-10. [PMID: 21118986 DOI: 10.1073/pnas.1016218107] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
MicroRNAs profoundly impact hematopoietic cells by regulating progenitor cell-fate decisions, as well as mature immune effector function. However to date, microRNAs that regulate hematopoietic stem cell (HSC) function have been less well characterized. Here we show that microRNA-125b (miR-125b) is highly expressed in HSCs and its expression decreases in committed progenitors. Overexpression of miR-125b in mouse HSC enhances their function, demonstrated through serial transplantation of highly purified HSC, and enriches for the previously described Slamf1(lo)CD34(-) lymphoid-balanced and the Slamf1(neg)CD34(-) lymphoid-biased cell subsets within the multipotent HSC (CD34-KLS) fraction. Mature peripheral blood cells derived from the miR-125b-overexpressing HSC are skewed toward the lymphoid lineage. Consistent with this observation, miR-125b overexpression significantly increases the number of early B-progenitor cells within the spleen and induces the expansion and enrichment of the lymphoid-balanced and lymphoid-biased HSC subset via an antiapoptotic mechanism, reducing the mRNA expression levels of two proapoptotic targets, Bmf and KLF13. The antiapoptotic effect of miR-125b is more pronounced in the lymphoid-biased HSC subset because of their intrinsic higher baseline levels of apoptosis. These effects of miR-125b are associated with the development of lymphoproliferative disease, marked by expansion of CD8(+) T lymphocytes. Taken together, these data reveal that miR-125b regulates HSC survival and can promote lymphoid-fate decisions at the level of the HSC by preferentially expanding lymphoid-balanced and lymphoid-biased HSC.
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